|
| Status |
Public on Feb 15, 2014 |
| Title |
Input_control |
| Sample type |
SRA |
| |
|
| Source name |
CAL-1 plasmacytoid dendritic cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: plasmacytoid dendritic cell
chip antibody: preimmune rabbit IgG (Bethyl Labs P120-101)
|
| Growth protocol |
The human CAL-1 plasmacytoid dendritic cell line was grown RPMI media supplemented with 10% FBS and 2mM L-Glutamine. Media was changed every 2-3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Input
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse hg18 genome using BWA version 0.5.9-r16.
Peaks were called using a Parzen window based algorithm (LEE et al, 2011. Nucleic Acis Res. 39(9):3558-73).
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak
|
| |
|
| Submission date |
Feb 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bum-Kyu Lee |
| E-mail(s) |
bklee92@gmail.com
|
| Phone |
512-232-8046
|
| Organization name |
University of Texas at Austin
|
| Street address |
2506 Speedway Stop A5000
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE55043 |
Dendritic Cell Fate is Determined by BCL11A Â |
|
| Relations |
| BioSample |
SAMN02642567 |
| SRA |
SRX471324 |
